LOTUS: Wikidata Query Results for Natural Products

The LOTUS Initiative dataset integrates chemical, biological, and bibliographic data from Wikidata. It contains four tables detailing chemical compounds, associated biological organisms, and their documenting references. This resource likely supports research linking natural product structures to their biological sources.

Use Cases

• Identifying natural products associated with specific biological taxa based on the compound_reference_taxon table.
• Retrieving chemical structure metadata (e.g., SMILES, InChI) for compounds from the compounds.tsv table.
• Linking chemical-biological associations to their source literature using the references.tsv metadata.
• Analyzing the taxonomic distribution of documented chemical compounds based on the taxa.tsv data.

Strengths

• Integrates data from the established LOTUS processing pipeline and broader Wikidata knowledge base.
• Provides structured links between chemical compounds, organisms, and scientific references.
• Includes multiple chemical structure representations (canonicalSMILES, isomericSmiles, inchi, inchiKey).

Limitations

• Key metadata such as row counts, dataset size, and last update date are unknown across all sources.
• The specific column names and data types for the four tables are not provided.
• The relationship between the LOTUS pipeline data and the broader Wikidata query results is not quantified.

Provenance

Source

University of Geneva (Adriano Rutz), via Wikidata and the LOTUS Initiative.

Collection Method

Results from a Wikidata query via the `downloadLotus` module of the lotus-wikidata-interact program.